Hooks are placed on a wrong origin
so, I watched the video but couldn't see the moment where he showed the origin of the hooks.

However, I think you should look into the "Set Origin"-options. You can open them by pressing "Space" and typing "Set Origin" into the appearing text box. Or just use the short cut "Shift + Alt + Ctrl + C".

Select all the hooks and choose one of the options. Try out whether one of them results in the wished origin position.

Greets
Jaspa

--- EDIT ------------------

Ohh god, I fixed it xD
You always tried to give the empty elements the origin. But first: empty elements have no origin, just a location (see my link in the comments for more details). And second: That's not what was  done in the tutorial.

To achieve the same origin as in the tutorial, you need to select the armatures (the whole bird) in Object Mode. Therefore you just need to click any bone. Once selected, you need to center the 3D cursor (as described in the comments too). Now you can use "set origin" options for applying the new origin. Et voilà: You've got the same settings as in your tutorial.

Have fun :)